Conservation genetics

Phylogenetics and population genetics lectures

• Key concepts and Single locus phylogenetics
• Multi-locus phylogenetics
• Population structure
• Conservation genetics
  • Theory
  • Methods
  • Discoveries

Molecular Ecology and Evolution at Bangor

• 3rd year module "Molecular ecology and evolution"
• Dissertation and MSc projects

• lecture material
• Relevant chapters in course textbooks (phylogenetics, population structure and conservation genetics)
• Overview of some of the discussed studies (plus any others you find)
• You may need to draw simple trees:
  • by hand and upload photo
  • newick format: ((human,chimp),cat)

Applied population genetics for the purpose of conservation

• Identifying management units
• Wildlife crime
• Population/ancestry assignment

In this lecture we will look at:

• Measuring loss of genetic diversity
  • Caused by drift in small populations
• Measuring inbreeding
  • Caused by mating with close relatives

• At small population sizes this overwhelms the rate of mutation, leading to net loss of diversity

Inbreeding depression

• Low diversity means recessive alleles of functional genes exposed in an increasingly homozygous state
• Deleterious alleles tend to be recessive
• For some loci, heterozygotes have higher fitness, can also be disrupted

Reduced evolutionary potential

• Selection acts on variants in the population driving adaptation
• Unpredictable because we don't know the future precisely (disease, climate change, etc)

• Mating between close relatives
• Not necessarily preferrential
• Becomes unavoidable in small populations
• Basically a form of drift
• Reduces diversity and evolutionary potential
• Effect on genome is more severe, and manifests in a single generation

Measuring diversity

• Many methods
• Heterozygosity is simple and often used
• Note across a large number of loci, heterozosity is same for all individuals in a population (HWE)

Getting data

• Traditionally a small number of markers (e.g. microsatellites) were used
• These would be selected based on being variable in the study population(s)
• Tends to overestimate diversity (circular reasoning)
• Things get unpredictable when applied to other populations/species
• Makes comparisons between species difficult to impossible

Barnett et al. 2020. Current Biology

• In theory can be calculated from know pedigrees (e.g. "pedigree" pets)
• Genetic approaches shown to be much more accurate
• Plus knowledge of pedigree not required
• In particular, genome sequencing allows identification of runs of homozygosity (ROH)